Methods development

The development of technologies in mass spectrometry allows deeper insights in the phenotypical status of cells. In parallel, further developments in the methods for sample preparation and measurement allows us to open new research fields and refine our analyses.

Global proteomics
Global proteomics aims to quantify thousands of proteins from biological matrices. The high complexity and the variety of protein abundances over several orders of magnitude are challenging. By combining different fractionation methods and by adapting the acquisition methods to the samples an enhanced quantification rate is accomplished and a focus on a specific protein subfraction is possible.
more: Johannes Schmidt ; Henning Großkopf ; Isabel Kratochvil
Post-translational modifications of proteins
The characterization of post-translational modifications (PTMs), e.g. protein phosphorylation, ubiquitination and acetylation, are the key in the understanding of an altered cellular signalling depending on external stimuli. The analysis of such PTMs necessitates an enrichment of modified proteins by different affinity purification strategies. Moreover, adaptions in the mass spectrometry acquisition methods and bioinformatic analysis are needed to identify the modification sites in proteins that allow the functional analysis of those modifications.

more: Johannes Schmidt ; Henning Großkopf
Targeted proteomics for absolute quantification
Targeted proteomics allows the identification as well as accurate and absolute quantification of proteins from complex biological matrices. This approach is used, if other methods, e.g. ELISA, are not possible, several proteins should be quantified from one sample or the sample amount is limited.
more: Laura Krieg
Metaproteomics of microbial communities

The objective of our experiments is the description of functional biodiversity within a microbial community. The small size of microorganisms and the difficult characterization of morphological and functional parameters make their direct investigation and differentiation difficult in mixed cultures. Using data on structural biodiversity (e.g. 16S rRNA gene sequencing), models will be developed to describe the system and possibly predict future bacterial community development.

more: Nico Jehmlich
Untargeted and targeted metabolomics
Targeted metabolomics enables the targeted identification and quantitation of small molecules based on MRM-spectra. This method offers a very robust and reliable way to analyze the abundance of metabolites in complex matrices.
As opposed to this, untargeted metabolomics depicts the entirety of all (measurable) metabolites and can unravel changes of the profile of different metabolites in biological samples. The comprehensive profiling of metabolites as well as the unbiased analysis represents the enormous strength of untargeted metabolomics.
more: Ulrike Rolle-Kampczyk ; Sven Haange ; Beatrice Engelmann
Metabolic Flux Analysis
As the sole abundance of metabolites is not always informative we are implementing a platform for metabolic flux analysis. For this purpose isotopically-labelled compounds are used and their fate through the metabolism can be followed using mass spectrometry. Using this technique accurate flux rates can be determined.
more: Beatrice Engelmann Katarina Fritz ; Isabel Kratochvil